Python

nwbinspector

Latest version: v0.4.23

PyUp actively tracks 471,271 Python packages for vulnerabilities to keep your Python environments secure.

Scan your dependencies

0.4.23

New Checks
* Added check `check_index_series_points_to_image` to additionally about future deprecation of `indexed_timeseries` linked in `IndexSeries`. [ 322](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/322)

0.4.22

Fixes
* Add a special skip condition to `check_timestamps_match_first_dimension` when an `IndexSeries` uses an `ImageSeries` as a target. [PR 321](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/321)

0.4.21

New Checks
* Added check for unique ids for DynamicTables. [PR 316](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/316)


Fixes
* Fix `check_subject_proper_age_range` to parse years. [PR 314](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/314)
* Write a custom `get_data_shape` method that does not return `maxshape`, which fixes errors in parsing shape. [PR 315](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/315)

0.4.20

Improvements

* Added compression size consideration to `check_image_series_size`. [PR 311](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/311)
* Added false positive skip condition for `check_image_series_size` for `TwoPhotonSeries` neurodata types. [PR 301](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/301)

Testing

* Added downstream testing of DANDI to the per-PR suite as a requirement for merging. [PR 306](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/306)

Fixes

* Fixed issue in `run_checks` following [PR 303](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/303) that prevented iteration over certain check output types. [PR #306](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/306)

0.4.19

Fixes

* Fixed an issue with table checks that attempted to retrieve data from on-disk NWB files in a non-lazy manner. Also improved `check_timestamps_match_first_dimension` for `TimeSeries` objects, which similarly attempted to load unnecessary data into memory. [PR 296](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/296) [PR #307](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/307)

0.4.18

Hotfix

* Fix to the assigned `importance` output of configured checks, which was reverting to pre-configuration values. [PR 303](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/303)

0.4.17

Hotfix

* Fix to skip certain tests if optional testing config path was not specified (mostly for conda-forge).

0.4.16

Improvements

* Allow NCBI taxonomy references for Subject.species. [PR 290](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/290)
* Added PyNWB v2.1.0 specific file generation functions to the `testing` submodule, and altered the tests for `ImageSeries` to use these pre-existing files when available. Also included automated workflow to push the generated files to a DANDI-staging server for public access. [PR 288](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/288)

Fixes

* Fixed relative path detection for cross-platform strings in `check_image_series_external_file_relative` [PR 288](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/288)

0.4.14

Fixes
* Fixed an error with attribute retrieval specific to the `cell_id` of the `IntracellularElectrode` neurodata type that occured with respect to older versions of PyNWB. [PR 264](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/264)

0.4.13

DANDI Configuration
* `check_subject_sex`, `check_subject_species`, `check_subject_age`, `check_subject_proper_age_range` are now elevated to `CRITICAL` importance when using the "DANDI" configuration. Therefore, these are now required for passing `dandi validate`.

Improvements
* Enhanced human-readability of the return message from `check_experimenter_form`. [PR 254](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/254)
* Extended check for ``Subject.age`` field with estimated age range using '/' separator. [PR 247](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/247)
* Allowed network-dependent tests to be skipped by specifying the `NWBI_SKIP_NETWORK_TESTS` environment variable. [PR 261](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/261)

New Checks
* Added check for existence of ``IntracellularElectrode.cell_id`` [PR 256](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/256)
* Added check that bounds of age range for ``Subject.age`` using the '/' separator are properly increasing. [PR 247](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/247)
* Added check for existence of ``IntracellularElectrode.cell_id`` [PR 256](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/256)
* Added check for shape consistency between ``reference_images`` and the x, y, (z) dimensions of the ``image_mask`` of ``PlaneSegmentation``objects. [PR 257](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/257)

Fixes
* Fixed the folder-wide `identifier` pre-check for `inspect_all` to read NWB files with extensions. [PR 262](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/262)

Links

Releases